Multiscale Modeling of Complex Systems Conformational Transitions in Proteins

Abstract

This project concerns development of new simulation methods for modeling protein conformational changes. The purpose is to develop accurate methods for generating a coarse Hamiltonian for use in Monte Carlo simulation. Our method is unique in that we derive the coarse scale energy function based on fine scale (all atom) simulation. We are developing a general scheme which employs both replica exchange (multiple temperatures) with resolution exchange (multiple scales). The method will lead to order-of-magnitude speedup in accurate simulations of loop conformations and protein folding more generally.

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Document Details

Document Type
Technical Report
Publication Date
Oct 14, 2006
Accession Number
ADA482429

Entities

People

  • David M Rogers
  • Nimal Wijesekera
  • Roman Petrenko
  • Thomas Beck

Organizations

  • University of Cincinnati

Tags

Communities of Interest

  • Energy and Power Technologies
  • Sensors

DTIC Thesaurus Topics

  • Abstracts
  • Algorithms
  • Amino Acids
  • Chemistry
  • Classification
  • Complex Systems
  • Computational Science
  • Databases
  • Dihedral Angle
  • Energy
  • Heat Capacity
  • Monte Carlo Method
  • Multiscale Modeling
  • Multiscale Simulations
  • Sampling
  • Simulations
  • Students

Readers

  • Molecular and Cellular Biochemistry
  • Neural Network Machine Learning.
  • Robotics and Automation.